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In one of the big rooms at the Battle Pike, Todd gasps in astonishment as he watches the body of the maiden disappear, and replaced by the mythical dragon Latias instead. Todd wants to know if the Pokémon is capable of morphing into humans, and a female voice suddenly speaks in his head to say it isn't the case. Todd's eyes widen with horror when he realizes that the voice comes from Latias, and the red dragon explains that she has come to support Emerald, and what he sees is the fake appearance she created by reflecting light with her down feathers.

Todd starts to go insane that he could hear a voice in his head, and Emerald states that Latias is just talking to him by telepathy, which is the way she communicates with humans. Latias grins that she has come to trust Todd, and knows that he will help them, which is why she decided to let him hear her words.

Latias then changes herself back into a maiden, and Todd, who has now calmed down from the shock, wants to know what they are planning to do. Emerald tells him to follow, and they soon arrive at the small room numbered 134. Upon entry, a wild Dusclops quickly throws itself against them, and the three narrowly evade.

Taking a good look at the ghost Pokémon, Emerald licks his lips and says it's birth place should be Mt. Pyre. With that, he pulls out his gun, and says the current soil will do the job. Todd has no idea why Emerald is mentioning about birth places and relating them to soils, and Latias explains that Emerald has travelled extensively across the land and has come into contact with various Pokémon. As a result, he can accurate point out the birth place of a Pokémon with one look, and the soil inside Emerald's gun right now is from the birth place of the Dusclops.

Emeralds wastes no time in firing off the soil bullets, and carves out a diamond shaped pattern on the ground. A mysterious glow instantly emanates from the bullet tracks, and in no time soothes Dusclops, who sits with a calm and content look on its face. Todd gasps that the same happened with Sudowoodo and Sceptile before, and bends down to pick up one of the soil bullets. He asks Emerald if it is really the soil from Dusclops's birth place, and Emerald grins that it is the soil from Mt. Pyre.

Latias explains that Emerald ties up the soil into bullets with special threads, which enables him to carve out an area on the ground which he calls a 'seal'. When the aroma of the soil washes over the Pokémon, the nostalgia of its birth place will soothe it and help it regain its mind. Todd is curious to know if Emerald possesses the soil of all the places he has visited, and the boy quickly holds out a thick tube which he keeps inside his sleeve with a tube connected to his gun. Todd sees that the tube is compartmentalized into many high-pressure small cartridges which are labelled with the names of different places, and is surprised that there are not only soils from Hoenn, but also from Kanto and Johto.

Emerald then pulls on Todd's hand, and says they must not waste time, as there are many more rampaging Pokémon waiting for him to cure. The three of them next head to room 88, and continue to sweep through all the small rooms where Emerald found suspicious wild Pokémon during his challenge. One by one, Emerald calms the Milotics, Sevipers, Kirlias and several other species with his soil gun. By the time he completes his task, it is already midnight.

Standing at the entrance of the Battle Pike, Emerald waves thank you to Latias as the red dragon returns to the skies. He then walks away himself, but Todd quickly stops him. The reporter remarks that while he now understands how Emerald calms the Pokémon in rampage, the core question still remains. He wants to know why there are such Pokémon at both the Battle Factory and Battle Pike, and back when Emerald mentioned that someone smuggled Sceptile into the Factory, who that someone could be.

Meanwhile, in the maintenance room of the Battle Factory, Noland lays unconscious on the ground. The man in armour grins that his work there is complete, but tells his Surskit that they must hurry, because only seven days are available for capturing Jirachi, and two have already passed. Looking down from the window, the man sees the press walking past the Factory, and says the current demonstration battle at the seven facilities following the Battle Frontier's opening ceremony has kept too many people at the place, making it difficult for him to carry out his actions.

Initially, he has placed rampaging Pokémon at the facilities to create danger, in hopes that the event will be suspended and the reporters will leave the Frontier. However, it seems that someone is interfering and messing up his plan. He wonders who it could be, but tells Surskit that while he doesn't know who the interferer is, whoever it is wouldn't be able to read their every move either. The armoured man seems amused that he and his opponent are both kept in the dark, and lets out a devilish giggle.

At the same time, walking east from the Battle Pike, Todd continues his incessant inquiry while trailing after Emerald. He demands to know who is mysterious suspect is, what his or her intention could be, whether Emerald is there to crack this evil scheme, who it was the sent him off to the Battle Frontier, and why the two mythical Pokémon, Latios and Latias, are helping him with his work.

Emerald holds up his hand to stop Todd, and decides to reveal what he knows. But just as he is about to explain, someone grabs him by the back of his clothes to lift him off the ground, and Todd cries that it is the mysterious suspect. However, the shadow walks into the light, and reveals itself to Brandon, who isn't too happy about being called a suspect. Todd realizes that it is just the Pyramid King, and is surprised to see the other reporters behind him, who have apparently been woken from their sleep.

Todd wonders what Brandon is doing there in the middle of the night, as the challenge is supposed to start the next day. Brandon grins that to cut it short, he has come to warn Emerald. Todd doesn't understand what he means, and the Pyramid King yells for the lights to be up. Powerful lights instantly come on to illuminate the Battle Pyramid, which happens to be just behind them, and the other reporters quickly set up their cameras to take snapshots of it shimmering in the dark.

Todd lets out a gasp at the sight of the magnificent building, and Brandon introduces it as the Battle Pyramid, the facility which calls for bravery. Emerald struggles to get free, and hollers that the man still hasn't explained what he is doing there. Brandon asks if Emerald remembers how long it took him to conquer his two previous challenges, and the boy recalls that the Factory took 15 hours while the Pike needed about 9 hours. Brandon grins that his point will soon be clear, and walks up the stairs to the Pyramid's entrace.

Without warning, he tosses the Emerald into the opening, who lands with his face hard on the ground. The boy quickly finds himself surrounded by complete darkness, and wonders if he is inside the Pyramid. He looks over to see Brandon standing at the entrance with a smirk, and the man tells him to find his way back in the dark. Emerald swiftly gets to his feet and starts walking, but finds himself coming against walls here and there just like a maze.

After a while, he manages to return to the entrance, and pants with exhaustion. Brandon tosses his three Pokéballs around, and grins that he expects better from him. The man then picks Emerald up and throws him into the opening again, and tells him to find his way out a second time. Emerald is annoyed that he needs to repeat what he did, and complains that finding the same route out is a no brainer to him.

However, he suddenly hits his face on a wall, and gasps in surprise as it wasn't there before. Brandon laughs that it is exactly what he was trying to illustrate, and states that his Battle Pyramid is also known as the maze of darkness, made up of dungeons which changes their layout at every entry. While it merely took half a day for Emerald to clear the Battle Factory and Pike, it will certainly require more than 24 hours for challengers to reach him inside the Pyramid, which is the warning he has come to give Emerald.

Todd realizes that it means Emerald will need more than a day to complete the Pyramid challenge, and he must start it tonight to keep up his pace of conquering one facility per day. Brandon states that challengers will be allowed to take three Pokémon with them, and the goal is to ascend the Pyramid by finding the stairs on each floor leading up. Excluding the top floor, the Pyramid is made up of a total of 7 storeys, and clearing them constitutes one cycle. Challengers may switch teams between each cycle, and Brandon himself will be waiting at the top after the tenth cycle.

Todd counts that Emerald need to get through 70 floors in order to challenge the Pyramid King, and Brandon adds that the challenge does not only involve finding a way out in the mazes, but there will also be virtual trainers and wild Pokémon waiting in the dark. Trainers will not be permitted to take their own items into the facility, and there will not be health restoration devices provided either. However, there are various items scattered inside the Pyramid, and challengers are free to pick them up for use.

Listening to the harsh rules, Todd knows that the challenge is even more difficult than the Factory and the Pike, and starts to get worried for Emerald. Brandon wants to know if Emerald has the bravery to accept the challenge after hearing the rules, and the boy states that he is not to kind to falter from hardship, claiming that he shall start his challenge at the Battle Pyramid right away. Brandon compliments on Emerald's boldness, and promises him a good adventure inside the Pyramid. The man beckons to the reporters to announce Emerald's decision, and welcomes them to stay and do coverage on the challenge.

Emerald then heads over to the PokémonCenter to prepare his team with Todd trailing after as usual. The reporter wonders if Emerald will be alright, and the boy playfully asks what he means. Todd gets annoyed, and points out that Emerald has just completed the Battle Pike challenge several hours ago, and says his exhausted body may not be able to put up with the tough requirements of the Pyramid which is going to last more than 24 hours.

Emerald brushes the matter off again like he always does, and Todd could do nothing but put on a frustrated look. Emerald accesses the computer to type in his choice of Pokémon, and says since he hasn't really planned on what to use, he will just make his decision based on the information he has learnt about the Pyramid a while ago.

A while later, Emerald returns to the Pyramid with an Alakazam, Phanpy and Shedinja. Brandon acknowledges the boy's team for the first cycle, and says as courtesy to challengers, he shall reveal his team lineup as well. Taking out the three Pokéballs which he always tosses around, he sends out the three Pokémon inside, and to Emerald shock, they are the legendary Regirock, Registeel and Regice…